相关论文: A Solvable Sequence Evolution Model and Genomic Co…
Textual analysis of typical microbial genomes reveals that they have the statistical characteristics of a DNA sequence of a much shorter length. This peculiar property supports an evolutionary model in which a genome evolves by random…
We introduce a simple model for DNA evolution. Using the method of Peng et al.$^1$, we investigate the fractal properties of the system. For small chains and chains of intermediate size we find a fractal exponent that indicates the…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
In this paper, we review the literature on statistical long-range correlation in DNA sequences. We examine the current evidence for these correlations, and conclude that a mixture of many length scales (including some relatively long ones)…
We study the stochastic dynamics of sequences evolving by single site mutations, segmental duplications, deletions, and random insertions. These processes are relevant for the evolution of genomic DNA. They define a universality class of…
The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic…
A simple growth model for DNA evolution is introduced which is analytically solvable and reproduces the observed statistical behavior of real sequences.
We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to…
A model of genome evolution is proposed. Based on three assumptions the evolutionary theory of a genome is formulated. The general law on the direction of genome evolution is given. Both the deterministic classical equation and the…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
We introduce a family of models incorporating random segmental substitutions and point mutations and demonstrate that such models reproduce algebraic length distributions of exact matches with the slope $-4$ observed earlier in pairwise…
Large scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of Life. Here we discuss approches of increasing complexity aimed at extracting…
The evolution model with parallel mutation-selection scheme is solved for the case when selection is accompanied by base substitutions, insertions, and deletions. The fitness is assumed to be either a single-peak function (i.e., having one…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
The study of correlation structure in the primary sequences of DNA is reviewed. The issues reviewed include: symmetries among 16 base-base correlation functions, accurate estimation of correlation measures, the relationship between $1/f$…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
The standard methods for detecting differential gene expression are mostly designed for analyzing a single gene expression experiment. When data from multiple related gene expression studies are available, separately analyzing each study is…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…